Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of the sequences of these clusters, we were able to link between sequence, structure, and disorder information. We introduced several parameters as measures of fluctuations at a given MSA site and used these as representative of the sequence and structure entropy at that site. In general, we found a tendency for negative correlations between disorder and structure, and significant positive correlations between disorder and the fluctuations in the system. We also found evidence for residue-type conservation for those residues proximate to potentially disordered sites. Mutation at the disorder site itself appear to be allowed. In addition, we found positive correlation for disorder and accessible surface area, validating that disordered residues occur in exposed regions of proteins. Finally, we also found that fluctuations in the dihedral angles at the original mutated residue and disorder are positively correlated while dihedral angle fluctuations in spatially proximal residues are negatively correlated with disorder. Our results seem to indicate permissible variability in the disordered site, but greater rigidity in the parts of the protein with which the disordered site interacts. This is another indication that disordered residues are involved in protein function.
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A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon’s Information Theory
We propose a framework to convert the protein intrinsic disorder content to structural entropy (H) using Shannon’s information theory (IT). The structural capacity (C), which is the sum of H and structural information (I), is equal to the amino acid sequence length of the protein. The structural entropy of the residues expands a continuous spectrum, ranging from 0 (fully ordered) to 1 (fully disordered), consistent with Shannon’s IT, which scores the fully-determined state 0 and the fully-uncertain state 1. The intrinsically disordered proteins (IDPs) in a living cell may participate in maintaining the high-energy-low-entropy state. In addition, under this framework, the biological functions performed by proteins and associated with the order or disorder of their 3D structures could be explained in terms of information-gains or entropy-losses, or the reverse processes.
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- NSF-PAR ID:
- 10137153
- Date Published:
- Journal Name:
- Entropy
- Volume:
- 21
- Issue:
- 6
- ISSN:
- 1099-4300
- Page Range / eLocation ID:
- 591
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The correlation between lattice chemistry and cation migration in high‐entropy Li+conductors is not fully understood due to challenges in characterizing anion disorder. To address this issue, argyrodite family of Li+conductors, which enables structural engineering of the anion lattice, is investigated. Specifically, new argyrodites, Li5.3PS4.3Cl1.7−
x Brx (0 ≤x ≤ 1.7), with varying anion entropy are synthesized and X‐ray diffraction, neutron scattering, and multinuclear high‐resolution solid‐state nuclear magnetic resonance (NMR) are used to determine the resulting structures. Ion and lattice dynamics are determined using variable‐temperature multinuclear NMR relaxometry and maximum entropy method analysis of neutron scattering, aided by constrained ab initio molecular dynamics calculations. 15 atomic configurations of anion arrangements are identified, producing a wide range of local lattice dynamics. High entropy in the lattice structure, composition, and dynamics stabilize otherwise metastable Li‐deficient structures and flatten the energy landscape for cation migration. This resulted in the highest room‐temperature ionic conductivity of 26 mS cm−1and a low activation energy of 0.155 eV realized in Li5.3PS4.3Cl0.7Br, where anion disorder is maximized. This study sheds light on the complex structure–property relationships of high‐entropy superionic conductors, highlighting the significance of heterogeneity in lattice dynamics. -
Intrinsically disordered regions (IDRs) carry out many cellular functions and vary in length and placement in protein sequences. This diversity leads to variations in the underlying compositional biases, which were demonstrated for the short vs. long IDRs. We analyze compositional biases across four classes of disorder: fully disordered proteins; short IDRs; long IDRs; and binding IDRs. We identify three distinct biases: for the fully disordered proteins, the short IDRs and the long and binding IDRs combined. We also investigate compositional bias for putative disorder produced by leading disorder predictors and find that it is similar to the bias of the native disorder. Interestingly, the accuracy of disorder predictions across different methods is correlated with the correctness of the compositional bias of their predictions highlighting the importance of the compositional bias. The predictive quality is relatively low for the disorder classes with compositional bias that is the most different from the “generic” disorder bias, while being much higher for the classes with the most similar bias. We discover that different predictors perform best across different classes of disorder. This suggests that no single predictor is universally best and motivates the development of new architectures that combine models that target specific disorder classes.more » « less
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Abstract Protein regions which are intrinsically disordered, exist as an ensemble of rapidly interconverting structures. Cooling proteins to cryogenic temperatures for dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR studies suspends most of the motions, resulting in peaks that are broad but not featureless. To demonstrate that detailed conformational restraints can be retrieved from the peak shapes of frozen proteins alone, we developed and used a simulation framework to assign peak features to conformers in the ensemble. We validated our simulations by comparing them to spectra of α‐synuclein acquired under different experimental conditions. Our assignments of peaks to discrete dihedral angle populations suggest that structural constraints are attainable under cryogenic conditions. The ability to infer ensemble populations from peak shapes has important implications for DNP MAS NMR studies of proteins with regions of disorder in living cells because chemical shifts are the most accessible measured parameter.
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Abstract Granulins (GRN 1‐7) are short (~6 kDa), cysteine‐rich proteins that are generated upon the proteolytic processing of progranulin (PGRN). These peptides, along with their precursor, have been implicated in multiple pathophysiological roles, especially in neurodegenerative diseases. Previously we showed that GRN‐3 and GRN‐5 are fully disordered in the reduced form implicating redox sensitive attributes to the proteins. Redox‐based modulations are often carried out by metalloproteins in mitigating oxidative stress and maintaining metal‐homeostasis within cells. To probe whether GRNs play a role in metal sequestration, we tested the metal binding propensity of the reduced forms of GRNs −3 and − 5 under neutral and acidic pH mimicking cytosolic and lysosomal conditions, respectively. We found, at neutral pH, both GRNs selectively bind Cu and no other divalent metal cations, with a greater specificity for Cu(I). Binding of Cu did not result in a disorder‐to‐order structural transition but partly triggered the multimerization of GRNs via uncoordinated cystines at both pH conditions. Overall, the results indicate that GRNs −3 and − 5 have surprisingly strong affinity for Cu in the pM range, comparable to other known copper sequestering proteins. The results also hint at a potential of GRNs to reduce Cu(II) to Cu(I), a process that has significance in mitigating Cu‐induced ROS cytotoxicity in cells. Together, this report uncovers metal‐coordinating property of GRNs for the first time, which may have profound significance in their structure and pathophysiological functions.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/e21060591
